Re: [AMBER] Alkali and Halide Monovalent Ion : paper

From: CHAMI F. <fatima.chami.durham.ac.uk>
Date: Tue, 6 Mar 2012 15:27:17 -0000

Hi Brian,

thank you so much for pointing me to this. I will rerun one system and see if the odd crystalisation does not occur for NaCl at 1 M

none of these frcmod is automatically loaded in tleap ...the default values are the one in parm99.dat (I copied them here)

 
  IM 2.47 0.1 Cl- Smith & Dang, JCP 1994,100:5,3757
  Li 1.1370 0.0183 Li+ Aqvist JPC 1990,94,8021. (adapted)
  IP 1.8680 0.00277 Na+ Aqvist JPC 1990,94,8021. (adapted)
  Na 1.8680 0.00277 Na+ Aqvist JPC 1990,94,8021. (adapted)
  K 2.6580 0.000328 K+ Aqvist JPC 1990,94,8021. (adapted)
  Rb 2.9560 0.00017 Rb+ Aqvist JPC 1990,94,8021. (adapted)
  Cs 3.3950 0.0000806 Cs+ Aqvist JPC 1990,94,8021. (adapted)
  MG 0.7926 0.8947 Mg2+ Aqvist JPC 1990,94,8021.(adapted)
  C0 1.7131 0.459789 Ca2+ Aqvist JPC 1990,94,8021.(adapted)

thanks
Fatima


-----Original Message-----
From: Brian Radak [mailto:radak004.umn.edu]
Sent: Mon 05/03/2012 17:28
To: AMBER Mailing List
Subject: Re: [AMBER] Alkali and Halide Monovalent Ion : paper
 
Hi Fatima,

I can't remember if these are yet the default parameters, but they are
easily loaded with the following frcmods:

frcmod.ionsjc_tip3p
frcmod.ionsjc_tip4pew
frcmod.ionsjc_spce

depending, of course, on which water model you have loaded (default is of
course TIP3P).

Regards,
Brian

On Mon, Mar 5, 2012 at 12:18 PM, CHAMI F. <fatima.chami.durham.ac.uk> wrote:

>
> Dear Dr. Thomas E. Cheatham
>
> I came across your article and I wonder if this new parameterization for
> Alkali and Halide Monovalent Ion has been implemented in the latest version
> of Amber ..I am currently using Amber 11 and Amber tools 1.4
>
> I had issues with NaCl and KCL for concentration greater than 1 M and
> 0.5 M respectively. using TIP3P water model ..with Amber 9
>
> Now I wish to rerun the same system but with the improved parameterization
>
> many thanks
> Fatima
>
>
> Determination of Alkali and Halide Monovalent Ion Parameters for Use in
> Explicitly
> Solvated Biomolecular Simulations
> In Suk Joung? and Thomas E. Cheatham, III*,?,?,
> Department of Bioengineering, College of Engineering, and
> Departments of Medicinal Chemistry and of
> Pharmaceutics and Pharmaceutical Chemistry, College of
> Pharmacy, UniVersity of Utah, 2000 South 30 East,
> Skaggs Hall 201, Salt Lake City, UT 84112
> ReceiVed: January 8, 2008; ReVised Manuscript ReceiVed: April
> 30, 2008
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>



-- 
================================ Current Address =======================
 Brian Radak                                             :     BioMaPS
Institute for Quantitative Biology
 PhD candidate - York Research Group       :     Rutgers, The State
University of New Jersey
 University of Minnesota - Twin Cities         :     Center for Integrative
Proteomics Room 308
 Graduate Program in Chemical Physics     :     174 Frelinghuysen Road,
 Department of Chemistry                          :     Piscataway, NJ
08854-8066
 radak004.umn.edu                                 :
radakb.biomaps.rutgers.edu
====================================================================
Sorry for the multiple e-mail addresses, just use the institute appropriate
address.
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Mar 06 2012 - 07:30:02 PST
Custom Search